Deciphering the genome structure and paleohistory of _Theobroma cacao_

We sequenced and assembled the genome of _Theobroma cacao_, an economically important tropical fruit tree crop that is the source of chocolate. The assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of them anchored on the 10 _T. cacao_ chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example flavonoid-related genes. It also provides a major source of candidate genes for _T. cacao_ disease resistance and quality improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten _T. cacao_ chromosomes were shaped from an ancestor through eleven chromosome fusions. The _T. cacao_ genome can be considered as a simple living relic of higher plant evolution

Characterization in silico of flavonoids biosynthesis in Theobroma cacao L.

A detailed and curated map of molecular interactions taking place in the polyphenols (flavonoids) biosynthesis in Theobroma cacao L. is presented. The map was created using the software Cytoscape v.2.7 and the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. The statistical parameters of the network were determined with CentiScape v.1.1 and MetaAnalyzer v.2.6.1. A preliminary theoretical map containing 1024 chemical species and 1099 chemical reactions was built, then a second map that was curated and annotated with the biological facts obtained from approximately 85 publications in T. cacao, with 653 chemical species and 706 chemical reactions. Structural analysis of this interaction network revealed similitude with other biological networks. The study of complex networks opens the way for creating realistic computational models of flavonoid biosynthesis metabolic pathways in cacao

The genome of Theobroma cacao.

We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions